RetrogeneDB ID: retro_mmul_884

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 11:82786255..82786768(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: TM2D3
• Ensembl ID: ENSMMUG00000000277
• Aliases: None
• Description: None

Sequence

>retro_mmul_884
TTGTGTAGCAGATATTCTGCAGACTTTATAGACTGCACAACAAATGTCCCCTGTGTCTATGGGAAGCTAGTCACTTTTGA
CTGTACAGTGAAACCTTCAGTTGCCTGTGTTGATTAAGAGTTAAAATACCAAAGTAACTTTATCATCAACATGACTTGAT
TTTGCTGGAATCTTCCAGAAACAGAATATGAATGTTTCAATTCTACCAGCTGCATAAAGTCCTGTCCTCAACTACATTAT
GCTGCCAACTGCTTGATCAACACATTCATGACTTGGGTAACTACTTTTTCCAAAATGCTGTACTGAAATTGGGCTGGAGG
CTGTAAGTGGTCTATTACTCTGGCTCTAAGCATCACCCTTGGTGGCTTTGGAGCAGATCATTTCTACCTCGACCAGTGGC
AAGAAGGCCTTGGCAAGCTCTTCAGCTTCAGTGGCCTGGAAATATGGACACTAATAGACATCTTGCTAATTGGAGTTGGC
TACATTGGACCAGCAGATGGCTCTTGATACATT

Alignment

ORF - retro_mmul_884 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.29 %
• Parental protein coverage: 70.85 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LCSRLPADCIDCTTNFSCIYGKPVTFDCAVKPSVTCVDQDFKSQKNFIINMTCRFCWQLPETDYECTNST
          LCSR..AD.IDCTTN..C.YGK.VTFDC.VKPSV.CVD...K.Q.NFIINMT..FCW.LPET.YEC.NST
Retrocopy LCSRYSADFIDCTTNVPCVYGKLVTFDCTVKPSVACVD*ELKYQSNFIINMT*-FCWNLPETEYECFNST

Parental  SCMTVSCPRQRYPANCTVRDHVHCLGNRTFPKMLYCNWTGGYKWSTALALSITLGGFGADRFYLGQWREG
          SC...SCP...Y.ANC............TF.KMLY.NW.GG.KWS..LALSITLGGFGAD.FYL.QW.EG
Retrocopy SCIK-SCPQLHYAANCLINTFMTWV--TTFSKMLY*NWAGGCKWSITLALSITLGGFGADHFYLDQWQEG

Parental  LGKLFSFGGLGIWTLIDVLLIGVGYVGPADGSLYI
          LGKLFSF.GL.IWTLID.LLIGVGY.GPADGS.YI
Retrocopy LGKLFSFSGLEIWTLIDILLIGVGYIGPADGS*YI

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	20.17 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	27.21 RPM
SRP007412_cerebellum	0.00 RPM	15.50 RPM
SRP007412_heart	0.00 RPM	10.83 RPM
SRP007412_kidney	0.00 RPM	10.80 RPM
SRP007412_liver	0.00 RPM	17.30 RPM
SRP007412_testis	0.00 RPM	11.80 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_884 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_884 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_884 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1138
Pan troglodytes	retro_ptro_775
Gorilla gorilla	retro_ggor_887

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017340	1 retrocopy	retro_cjac_3233,
Homo sapiens	ENSG00000184277	1 retrocopy	retro_hsap_1138,
Gorilla gorilla	ENSGGOG00000011598	1 retrocopy	retro_ggor_887,
Macaca mulatta	ENSMMUG00000000277	1 retrocopy	retro_mmul_884 ,
Mustela putorius furo	ENSMPUG00000010985	1 retrocopy	retro_mputfur_313,
Nomascus leucogenys	ENSNLEG00000000529	1 retrocopy	retro_nleu_937,
Pan troglodytes	ENSPTRG00000007515	1 retrocopy	retro_ptro_775,
Tarsius syrichta	ENSTSYG00000004536	1 retrocopy	retro_tsyr_1116,